[FEATURE] Accept user-defined tags #3256
Conversation
|
The latest updates on your projects. Learn more about Vercel for Git ↗︎
|
eseiler
force-pushed
the
feature/user_tags
branch
from
72f288d
to
88e8642
Compare
seqan-actions
added
lint
| { | ||
| consume_unsupported_tag_and_print_warning("HD", raw_tag); | ||
| parse_and_append_unhandled_tag_to_string(hdr.user_tags, raw_tag); |
There was a problem hiding this comment.
Just for me to understand the format here. We store all parsed line field tags tab separated within a string. Or are official field tags from the specification stored in a different format?
There was a problem hiding this comment.
All the header stuff (SQ, HD, RG) have strutcs that store the members defined in the SAM spec. Any user defined tags are stored as string. For the alignment records, tags, including User-defined, are stored in the SAM tag dictionary.
There was a problem hiding this comment.
Yes, but do I see it right that here we store the user defined field tags in a tab seperated string? If so, I feel like it would make more sense to put this into a vector of field tags instead.
There was a problem hiding this comment.
Yes, that would be better. Would be nice to store a struct with the name and value.
Anyway, I would do it as a followup, because it breaks api for the header tags where we already store the user tags in a string (SQ and RG).
If we do a vector, we should also throw on invalid formatting (it should be TAG:VALUE with some constraints on allowed characters) like samtools does.
There was a problem hiding this comment.
Sounds good! Would you mind tracking this on the issue board?
There was a problem hiding this comment.
Will do when working on this issue
eseiler
force-pushed
the
feature/user_tags
branch
from
88e8642
to
32112bd
Compare
seqan-actions
added
lint
eseiler
force-pushed
the
feature/user_tags
branch
from
697070f
to
d0eabcf
Compare
seqan-actions
added
lint
|
Documentation preview available at https://docs.seqan.de/preview/seqan/seqan3/3256 |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #3256 +/- ##
==========================================
- Coverage 98.14% 98.13% -0.01%
==========================================
Files 271 271
Lines 11955 11951 -4
Branches 104 104
==========================================
- Hits 11733 11728 -5
- Misses 222 223 +1 ☔ View full report in Codecov by Sentry. |
Resolves #3251